--Ap Bio Chapter 16

Front 1

T/F: Of all nature's molecules, nucleic acids are unique in their ability to direct their own replication from monomers.

Back 1

True

Front 2

T/F: Until the 1940s, the heterogeneity and specificity of function of proteins made them a likely candidate for being the basis of inheritance and DNA

Back 2

True

Front 3

When British Frederick Griffith mixed a dead group of the pathogenic strain of pneumonia with an alive group of the non-pathogenic strain, what happened and what was this called?

Back 3

The non-pathogenic strains all subsequently became pathogenic. Grifith called this "transformation."

Front 4

What is the official definition of a transformation (separate from the transformation of a normal cell into a cancerous cell as from chapter 12)?

Back 4

When a change in genotype and then phenotype occurs due to the assimilation of external DNA by a cell

Front 5

How did Oswald Avery discover that in bacteria the heritable factor that transformed the pneumonia prokaryotes from pathogenic to non pathogenic was DNA?

Back 5

He had chemicals that inactivated DNA, RNA, and protein, and only when DNA was activated was transformation allowed to occur.

Front 6

Why did virtually no one care about Oswald's discovery during his time?

Back 6

Bc most people believed that proteins were more complex & thus the basis of heredity and most people thought human heredity was much different than bacteria heredity

Front 7

Describe bateriophages, or phages, such as T2, and what they do.

Back 7

They are viruses that "eat" bacteria and are only composed of DNA and protein. They attach to their host and cause it to produce many many more T2 phages, somehow altering the host's hereditary mechanisms.

Front 8

Why was the Hershey-Chase experiment so groundbreaking?

Back 8

Bc the use of radioactive tracers showed that the DNA of a phage entered the host cell and caused the mutation, not the protein. It showed that DNA was the molecular basis of inheritance, at least for viruses.

Front 9

How did Erwin Chargaff perform an important experiment?

Back 9

He showed that different species had different percentages of each amount of base pair in their DNA, which gave DNA more credibility as the diverse molecular basis of inheritance.

Front 10

What was the second important discovery made by Chargoff?

Back 10

That Adenine and thymine, and then cytosine and guanine are present in equal percentages in all organisms.

Front 11

How did Watson initially come up with his "two strand" molecule?

Back 11

He visited the lab of Wilkins and Rosalind franklin and from their crystallography (study of 3-D structures by the use of X-rays) he determined that DNA was helical & (by studying the width of the helix) he found that it was a double stranded, not triple stranded as some people had suggested.

Front 12

How many layers of base pairs, or rungs of the ladder, are there in each full turn of the helix?

Back 12

10

Front 13

Other than using Rosalind Franklin's crystallography, how else did Watson and Crick basically rip her off?

Back 13

They used her unpublished report which proved that the phosphate group and sugar were on the outside of the double helix bc they are hydrophilic and base pairs are hydrophobic

Front 14

How did Watson and Crick know that A didn't pair with A, and so on?

Back 14

Bc the crystallography suggested that the width of DNA was uniform. A and G are purines & are about twice as long as T and C which are pyrimidines. If A paired with A and T with T, DNA would not be of uniform width

Front 15

How did Watson and Crick reason that there must be additional specificity in the pairing of nitrogenous bases?

Back 15

Bc A only forms two hydrogen bonds with T, and G only forms three hydrogen bonds with C; not just any purine can combine with any pyrimidine

Front 16

When referring to the 5' and 3' ends of DNA, we are talking about the ULTIMATE ends of the sugar, not in between. What does the 5' end have and what does the 3' end have?

Back 16

5' has the P group, 3' has the OH group.

Front 17

What is the semi-conservative model and what were the two other possibilities of models proposed before the semi-c was proven?

Back 17

This model says that one strand of parent DNA molecule and a new complementary strand make up DNA after replication. The conservative model says that the parent molecule is always conserved and somehow binds back up after replication, and the dispersive model says that all four separate strands of DNA have a mixture of old and new DNA.

Front 18

Matthew Meselson and Franklin Stahl confirmed...

Back 18

The semi-conservative model of DNA replication

Front 19

Short stretches of DNA having a specific sequence of nucleotides where the replication of a DNA molecule begins are called...

Back 19

Origins of replication

Front 20

T/F: DNA replication proceeds in both directions from the origin of replication in all cells

Back 20

True

Front 21

In eukaryotes, what completes basic DNA replication?

Back 21

When all the linear replication bubbles keep growing in both directions and the replication forks finally fuse and the bubbles are together, then DNA replication is complete and the old 2 strands of the parent molecule are completely separate

Front 22

What protein helps unwind and separate the strands of the single DNA molecule at the replication fork?

Back 22

Helicase

Front 23

What molecules bind to the UNPAIRED DNA strands of DNA during replication and stabilizes them?

Back 23

Single-strand binding proteins

Front 24

What molecules bind to the full, unseparated strand of DNA ahead of the replication fork? What does it do and why?

Back 24

The untwisting of DNA at the replication fork causes tighter twisting ahead of the fork, so topoisomerase helps to relieve this strain by breaking, swiveling, etc.

Front 25

What is an RNA primer, what does it do, and what makes it?

Back 25

Primase makes the RNA primer, about 10 bases of RNA which INITIATE the copying of DNA. After primase makes the RNA primer and binds it to the DNA molecule with respective base pairs, DNA-bearing enzymes can start the total copying of the DNA.

Front 26

Describe the structure of a nucleoside triphosphate.

Back 26

A sugar, a nitrogenous base, and 3 phosphate groups.

Front 27

Explain what happens when each nucleotide added to a parent strand of DNA for replication comes from a nucleoside.

Back 27

2 P groups from the nucleoside are lost to form pyrophosphate which is hyrdolyzed in an exergonic reaction which helps fuel the polymerization process of all the new base pairs. The remaining parts of the nucleoside create the single phosphate group, sugar, and base that make up a normal strand of DNA.

Front 28

In E. coli, what adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides along the replication fork?

Back 28

DNA polymerase III

Front 29

T/F: Bc of its structure, DNA polymerase can ONLY add nucleosides/nucleotides to a parent strand of DNA in the 5' to 3' direction, which is cool for one direction of the replication fork, but not okay for the other

Back 29

True

Front 30

Bc DNA polymerase can only replicate in the 5' -> 3' direction, and the replication fork goes both ways down the 2 parent strands of a DNA molecule, what is the easy strand called that already goes from the 5' to 3' direction? How many RNA primers are necessary?

Back 30

The leading strand; only 1 RNA primer is needed

Front 31

The DNA strand that DNA polymerase III has to replicate AWAY from the replication fork so that it can follow its 5' to 3' direction is called the...

Back 31

Lagging strand

Front 32

T/F: The lagging strand is elongated discontinuously in a series of segments

Back 32

True

Front 33

EACH of the 2 DNA strands in a parent DNA molecule has leading and lagging strands. Why?

Back 33

Because the replication fork goes in BOTH ways, so the 5' -> 3' strand (from top to bottom) will have replication going in both ways when in reality the DNA poly III can only replicate from the 5' to 3' direction

Front 34

The segments of the lagging strand that are created during replication are called...

Back 34

Okazaki fragments

Front 35

After RNA primase primes the individual Okazaki fragments of the lagging strand, what molecule replaces the RNA with copies of DNA, adding them one by one onto the 3' end of the fragment?

Back 35

DNA polymerase I

Front 36

Although DNA Poly I replaces the RNA primer with DNA, it cannot join the two Okazaki segments to create a full strand. What ultimately does this?

Back 36

DNA ligase

Front 37

What is the "sliding clamp"? What does it do?

Back 37

The sliding clamp is the protein that follows behind DNA poly III while the poly III adds nucleotides/nucleosides to the parent strand of DNA. It physically moves DNA poly III along the DNA template strand

Front 38

Why isn't a model of the proteins associated with DNA replication moving along DNA like a railroad track plausible?

Back 38

Bc all the proteins are actually together in a complex and bc the DNA being replicated is actually "pulled thru" the complex, while the complex remains still and unmoving in the nuclear matrix

Front 39

If a mismatch pair of nucleotide bases is created during DNA replication and evades the proofreading of the DNA polymerase, what happens and what is important about this?

Back 39

If this happens, enzymes remove and replace incorrectly paired nucleotides that have resulted in replication errors. These enzymes are important bc genetic defects that lead to their absence has been directly shown to cause colon cancer.

Front 40

T/F: Bc of spontaneous or environmental mutation factors, the DNA in each cell even before or after replication is constantly monitored and repaired by the cell.

Back 40

True

Front 41

Briefly explain a nucleotide excision repair.

Back 41

When damage is detected, a nuclease enzyme cuts out one segment of the damaged strand, DNA poly adds new bases, and DNA ligase finally binds the new molecule together.

Front 42

In what situations are thymine dimers usually created?

Back 42

They are usually created from damage from UV light

Front 43

Special, often short, repeating nucleotide sequences at the ends of linear DNA that protect from eventual DNA erosion yet use proteins in order to not trigger damage pathways are called...

Back 43

Telomeres

Front 44

If the chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce. Why doesn't this actually every occur?

Back 44

Bc the enzyme telomerase lengthens telomeres in eukaryotic germ cells, which make gametes (sex cells) with telomeres of longest possible length

Front 45

T/F: Normal shortening of telomeres may protect organisms from cancer by limiting the number of divisions that regular cells can undergo.

Back 45

True

Front 46

T/F: The presence of telomerase in many cancer cells suggests that it (obviously) allows more replication to occur than should be possible and could be the cause of constantly-replicating cancer

Back 46

True

Front 47

The dense region of DNA in a bacterium unlike that of eukaryotic cells is called a nucleoid, and is...

Back 47

Not bound by a membrane

Front 48

The complex of DNA and protein that fits into the nucleus through an elaborate, multilevel system of DNA packing is called...

Back 48

Chromatin

Front 49

T/F: Although histone proteins are small, their mass is about exactly equivalent to the mass of total DNA in a nucleus

Back 49

True

Front 50

Why do histones readily bind to a linear DNA molecule?

Back 50

Bc they are positively charged with their amino acids and the P groups on DNA make it negatively charged

Front 51

Each bead between the 10nm chromatin strands is called a _, the basic unit of DNA packaging.

Back 51

Nucleosome

Front 52

The "string" between the beads of nucleosomes of chromatin is called...

Back 52

Linker DNA

Front 53

T/F: DNA rarely leaves the histone-cluster in a nucleoside

Back 53

True

Front 54

What is the 30nm fiber?

Back 54

When the nucleosides get together due to the interactions of histone tails and form a big coil of nucleosides and linker DNA

Front 55

When the 30nm fiber forms loops and is attached to a "chromosome scaffold" made of proteins, this is called...

Back 55

A looped domain

Front 56

T/F: The looped domains often lack a definite scaffold but may be attached to the nuclear lamina or the nuclear matrix which helps organize regions of chromatin, and even when chromatin is just in a big heap of DNA individual chromosomes do not become entangled

Back 56

True

Front 57

What is the difference between heterochromatin and euchromatin?

Back 57

Heterochromatin is the big ball of centromeres and telomeres that heaps up even during interphase and thus cannot usually be used during gene expression. Euchromatin is the rest of the cell's DNA which is not very coiled up during interphase and can thus be used for gene expression